ABSTRACT Familial adenomatous polyposis (FAP) is an autosomal dominant inherited disorder caused by a germline mutation in the adenomatous polyposis coli (APC) gene, leading to a nearly 100% risk of colorectal cancer and a 12% lifetime risk of duodenal cancer. Since prophylactic colectomy is now the standard of care when colorectal polyposis increases beyond endoscopic management, duodenal cancer has now become the leading cause of death in FAP. Efficacious chemoprevention of duodenal neoplasia is, therefore, an unmet clinical need. As part of a Phase II double blind, randomized placebo-controlled trial (FAPEST trial) of sulindac and erlotinib therapy in FAP patients, we showed a profound 38% decrease in duodenal polyp burden at 6 months (P=4.2 X 10-12). However, the mechanisms by which COX and EGFR inhibition protects against duodenal neoplasia remain incompletely understood. In addition the high rate of adverse reactions limits its clinical application. We propose to use state-of-the art metabolomic strategies to discern the underlying mechanisms of this striking chemopreventive response to sulindac-erlotinib and to identify biomarkers that will bring this effective combination to clinical application. Specific aims are: (1) Identification of changes in the duodenal metabolomic profile associated with sulindac and erlotinib therapy in patients with FAP and (2) identification of novel metabolomic markers associated with chremopreventive response to sulindac and erlotinib in patients with FAP. As part of a collaboration with the NIH West Coast Metabolomics Center we will use a set of 52 FAP patients from the FAPEST trial and characterize the normal duodenal tissue with respect to both targeted and untargeted metabolomics. Specifically, we will use the following three technology platforms to detect both identified and ?novel? metabolite signals which will provide further mechanistic understanding and innovate biomarkers: 1. Complex lipids by CSH-QTOF mass-spectrometry (MS) (n=350 lipids); 2. Primary metabolites such as amino acids, sugars and hydroxyl acids by GCTOF MS (n=170); and 3. Oxylipin analysis by UPLC-QTrap MS (n=30). This study is unique in that it builds on a highly successful chemoprevention trial to 1) identify biologic mechanisms that inhibit gastrointestinal carcinogenesis and 2) to develop indicators of response and adverse reactions. This work may have impact beyond FAP to sporadic CRC where somatic APC mutations are highly prevalent. It will also be the first in vivo metabolomic profiling of the effects of erlotinib, a broadly used chemotherapeutic drug. Finally, it will provide proof-of-principle of the use of metabolomics in chemoprevention studies. We anticipate that the metabolomic profiles identified could be rapidly tested in subsequent chemoprevention trials and subsequently adopted into clinical practice with clear near-term impact on management of FAP patients.